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root/group/trunk/OOPSE/libmdtools/Integrator.hpp
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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 561 by mmeineke, Fri Jun 20 20:29:36 2003 UTC vs.
Revision 693 by tim, Wed Aug 13 19:21:53 2003 UTC

# Line 1 | Line 1
1   #ifndef _INTEGRATOR_H_
2   #define _INTEGRATOR_H_
3  
4 + #include <string>
5 + #include <vector>
6   #include "Atom.hpp"
7 + #include "Molecule.hpp"
8   #include "SRI.hpp"
9   #include "AbstractClasses.hpp"
10   #include "SimInfo.hpp"
11   #include "ForceFields.hpp"
12   #include "Thermo.hpp"
13   #include "ReadWrite.hpp"
14 + #include "ZConsWriter.hpp"
15  
16 + using namespace std;
17   const double kB = 8.31451e-7;// boltzmann constant amu*Ang^2*fs^-2/K
18   const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
19 + const double p_convert = 1.63882576e8; //converts amu*fs^-2*Ang^-1 -> atm
20   const int maxIteration = 300;
21   const double tol = 1.0e-6;
22  
17 – class Integrator : public BaseIntegrator {
23  
24 + template<typename T = BaseIntegrator> class Integrator : public T {
25 +
26   public:
27    Integrator( SimInfo *theInfo, ForceFields* the_ff );
28    virtual ~Integrator();
# Line 31 | Line 38 | class Integrator : public BaseIntegrator { (protected)
38    virtual void constrainA( void );
39    virtual void constrainB( void );
40    virtual int  readyCheck( void ) { return 1; }
41 +
42 +  virtual void calcForce( int calcPot, int calcStress );  
43 +  virtual void thermalize();
44    
45    void checkConstraints( void );
46    void rotate( int axes1, int axes2, double angle, double j[3],
47 <               double A[9] );
48 <
39 <
47 >               double A[3][3] );
48 >              
49    ForceFields* myFF;
50  
51    SimInfo *info; // all the info we'll ever need
# Line 62 | Line 71 | class Integrator : public BaseIntegrator { (protected)
71    double dt;
72    double dt2;
73  
65 –  double* pos;
66 –  double* vel;
67 –  double* frc;
68 –  double* trq;
69 –  double* Amat;
70 –
74    Thermo *tStats;
75    StatWriter*  statOut;
76    DumpWriter*  dumpOut;
77    
78   };
79  
80 < class NVE : public Integrator{
80 > typedef Integrator<BaseIntegrator> RealIntegrator;
81  
82 + template<typename T> class NVE : public T {
83 +
84   public:
85    NVE ( SimInfo *theInfo, ForceFields* the_ff ):
86 <    Integrator( theInfo, the_ff ){}
87 <  virtual ~NVE(){}
83 <
84 <  
85 <
86 >    T( theInfo, the_ff ){}
87 >  virtual ~NVE(){}  
88   };
89  
88 – class NVT : public Integrator{
90  
91 + template<typename T> class NVT : public T {
92 +
93   public:
94  
95    NVT ( SimInfo *theInfo, ForceFields* the_ff);
96    virtual ~NVT() {}
97  
95 –  void setQmass(double q) {qmass = q; have_qmass = 1;}
98    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
99    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
100  
# Line 103 | Line 105 | class NVT : public Integrator{ (protected)
105  
106    virtual int readyCheck();
107  
108 <  // zeta is a propagated degree of freedom.
108 >  // chi is a propagated degree of freedom.
109  
110 <  double zeta;
110 >  double chi;
111  
112 <  // targetTemp must be set.  One of qmass or tauThermostat must be set;
112 >  // targetTemp must be set.  tauThermostat must also be set;
113  
112 –  double qmass;
114    double targetTemp;
115    double tauThermostat;
115 –
116 –  double NkBT;
116    
117 <  short int have_tau_thermostat, have_target_temp, have_qmass;
117 >  short int have_tau_thermostat, have_target_temp;
118  
119   };
120  
121  
123 – class NPT : public Integrator{
122  
123 + template<typename T> class NPTi : public T{
124 +
125   public:
126  
127 <  NPT ( SimInfo *theInfo, ForceFields* the_ff);
128 <  virtual ~NPT();
127 >  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
128 >  virtual ~NPTi() {};
129  
130 <  void setQmass(double q) {qmass = q; have_qmass = 1;}
130 >  virtual void integrateStep( int calcPot, int calcStress ){
131 >    calcStress = 1;
132 >    T::integrateStep( calcPot, calcStress );
133 >  }
134 >
135    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
136    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
137    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
# Line 140 | Line 144 | class NPT : public Integrator{ (protected)
144  
145    virtual int readyCheck();
146  
147 <  Atom** atoms;
147 >  // chi and eta are the propagated degrees of freedom
148  
149 <  // zeta and epsilonDot are the propagated degrees of freedom.
149 >  double chi;
150 >  double eta;
151 >  double NkBT;
152  
153 <  double zeta;
154 <  double epsilonDot;
153 >  // targetTemp, targetPressure, and tauBarostat must be set.  
154 >  // One of qmass or tauThermostat must be set;
155  
156 +  double targetTemp;
157 +  double targetPressure;
158 +  double tauThermostat;
159 +  double tauBarostat;
160 +
161 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
162 +  short int have_target_pressure;
163 +
164 + };
165 +
166 + template<typename T> class NPTim : public T{
167 +
168 + public:
169 +
170 +  NPTim ( SimInfo *theInfo, ForceFields* the_ff);
171 +  virtual ~NPTim() {};
172 +
173 +  virtual void integrateStep( int calcPot, int calcStress ){
174 +    calcStress = 1;
175 +    T::integrateStep( calcPot, calcStress );
176 +  }
177 +
178 +  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
179 +  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
180 +  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
181 +  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
182 +
183 + protected:
184 +
185 +  virtual void moveA( void );
186 +  virtual void moveB( void );
187 +
188 +  virtual int readyCheck();
189 +
190 +  Molecule* myMolecules;
191 +  Atom** myAtoms;
192 +
193 +  // chi and eta are the propagated degrees of freedom
194 +
195 +  double chi;
196 +  double eta;
197 +  double NkBT;
198 +
199    // targetTemp, targetPressure, and tauBarostat must be set.  
200    // One of qmass or tauThermostat must be set;
201  
153 –  double qmass;
202    double targetTemp;
203    double targetPressure;
204    double tauThermostat;
205    double tauBarostat;
206  
207    short int have_tau_thermostat, have_tau_barostat, have_target_temp;
208 <  short int have_target_pressure, have_qmass;
208 >  short int have_target_pressure;
209 >
210 > };
211 >
212 > template<typename T> class NPTf : public T{
213 >
214 > public:
215 >
216 >  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
217 >  virtual ~NPTf() {};
218 >
219 >  virtual void integrateStep( int calcPot, int calcStress ){
220 >    calcStress = 1;
221 >    T::integrateStep( calcPot, calcStress );
222 >  }
223 >
224 >  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
225 >  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
226 >  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
227 >  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
228 >
229 > protected:
230 >
231 >  virtual void  moveA( void );
232 >  virtual void moveB( void );
233 >
234 >  virtual int readyCheck();
235 >
236 >  // chi and eta are the propagated degrees of freedom
237  
238 +  double chi;
239 +  double eta[3][3];
240 +  double NkBT;
241 +
242 +  // targetTemp, targetPressure, and tauBarostat must be set.  
243 +  // One of qmass or tauThermostat must be set;
244 +
245 +  double targetTemp;
246 +  double targetPressure;
247 +  double tauThermostat;
248 +  double tauBarostat;
249 +
250 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
251 +  short int have_target_pressure;
252 +
253   };
254  
255 + template<typename T> class NPTfm : public T{
256 +
257 + public:
258 +
259 +  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
260 +  virtual ~NPTfm() {};
261 +
262 +  virtual void integrateStep( int calcPot, int calcStress ){
263 +    calcStress = 1;
264 +    T::integrateStep( calcPot, calcStress );
265 +  }
266 +
267 +  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
268 +  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
269 +  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
270 +  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
271 +
272 + protected:
273 +
274 +  virtual void  moveA( void );
275 +  virtual void moveB( void );
276 +
277 +  virtual int readyCheck();
278 +
279 +  Molecule* myMolecules;
280 +  Atom** myAtoms;
281 +
282 +  // chi and eta are the propagated degrees of freedom
283 +
284 +  double chi;
285 +  double eta[3][3];
286 +  double NkBT;
287 +
288 +  // targetTemp, targetPressure, and tauBarostat must be set.  
289 +  // One of qmass or tauThermostat must be set;
290 +
291 +  double targetTemp;
292 +  double targetPressure;
293 +  double tauThermostat;
294 +  double tauBarostat;
295 +
296 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
297 +  short int have_target_pressure;
298 +
299 + };
300 +
301 + template<typename T> class ZConstraint : public T {
302 +
303 + public:
304 +
305 +  ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
306 +  ~ZConstraint();
307 +    
308 +  void setZConsTime(double time)                  {this->zconsTime = time;}
309 +  void getZConsTime()                             {return zconsTime;}
310 +  
311 +  void setIndexOfAllZConsMols(vector<int> index)  {indexOfAllZConsMols = index;}
312 +  void getIndexOfAllZConsMols()                   {return indexOfAllZConsMols;}
313 +  
314 +  void setZConsOutput(const char * fileName)      {zconsOutput = fileName;}
315 +  string getZConsOutput()                         {return zconsOutput;}
316 +  
317 +  virtual void integrate();
318 +  
319 +
320 + #ifdef IS_MPI
321 +  virtual void update(); //which is called to indicate the molecules' migration
322   #endif
323 +
324 + protected:
325 +
326 +  enum ZConsState {zcsMoving, zcsFixed};
327 +
328 +
329 +
330 +  virtual void calcForce( int calcPot, int calcStress );
331 +  virtual void thermalize(void);
332 +  
333 +  void zeroOutVel();
334 +  void doZconstraintForce();
335 +  void doHarmonic();
336 +  bool checkZConsState();
337 +
338 +  bool haveFixedZMols();
339 +  bool haveMovingZMols();
340 +
341 +  double calcZSys();
342 +
343 +  int isZConstraintMol(Molecule* mol);
344 +
345 +
346 +  double zconsTime;
347 +  double zconsTol;
348 +  double zForceConst;
349 +  
350 +  vector<Molecule*> zconsMols;
351 +  vector<double> massOfZConsMols;
352 +  vector<double> kz;
353 +  vector<ZConsState> states;
354 +  vector<double> zPos;
355 +  
356 +  
357 +  vector<Molecule*> unconsMols;
358 +  vector<double> massOfUnconsMols;
359 +  double totalMassOfUncons;
360 +
361 +  vector<ZConsParaItem>* parameters;
362 +  
363 +  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
364 +
365 +  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules  
366 +  double* fz;
367 +  
368 +  int totNumOfUnconsAtoms;
369 +
370 +  int whichDirection;                           //constraint direction
371 +  
372 + private:
373 +  
374 +  string zconsOutput;
375 +  ZConsWriter* fzOut;
376 +
377 +  double calcCOMVel();
378 +  double calcCOMVel2();
379 +
380 + };
381 +
382 + #endif

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